Oh, and one more thing, when you install the tools through the playbook, do
they appear in the admin section?

On 21 April 2016 at 19:37, Marius van den Beek <m.vandenb...@gmail.com>
wrote:
> Okay, that was a bit too short for the tool_list.yml.
> What is important is that you either have the tool_panel_section_label or
> tool_panel_section_id included in your tool_list.yml (for each tool!).
> Then it would help us to see what is going on if you can run the playbook
> with the -vvvv parameter, as well as what is going on at the same time in
> your galaxy logs.
>
> On 21 April 2016 at 19:30, William Ge <w...@centrilliontech.com> wrote:
>
>> Thanks, Marius!
>>
>>
>>
>> Sure, here it is:
>>
>> I followed the online instructions to git clone the master Galaxy (Feb.,
>> 2016) and configured it for local production use with PostgreSQL and
>> proftp. First tried ansible to install the tools, but did not succeed. Then
>> tried the online admin installation of tools one-by-one. That worked, and I
>> installed at least one tool for each section this way. With more help from
>> you and others later, I got ansible-playbook to run to install the tools.
>> That ran OK, but did not see the tools installed show up on the web
>> frontend.
>>
>>
>>
>> Beginning of the tool_list.yml is the same as the one included in the
>> playbook/roles, except for the api_key and galaxy_instance:
>>
>>
>>
>> api_key: ‘d22b682…’
>>
>> galaxy_instance: 127.0.0.1:8080
>>
>> tools:
>>
>> - name: ‘column_maker’
>>
>> owner: …
>>
>>
>>
>>
>>
>> The command I used is: ansible-playbook tools.yaml
>>
>> The playbook was downloaded end of March, following the link given on the
>> Galaxy tool installation guide.
>>
>> Manual installation of the tools one-by-one from the Admin web page
>> works. The tools installed show up on the web page.
>>
>>
>>
>> Thanks,
>>
>> Bill
>>
>> *From:* Marius van den Beek [mailto:m.vandenb...@gmail.com]
>> *Sent:* Thursday, April 21, 2016 9:45 AM
>> *To:* William Ge <w...@centrilliontech.com>
>> *Cc:* Enis Afgan <enis.af...@irb.hr>; galaxy-dev@lists.galaxyproject.org
>>
>> *Subject:* Re: [galaxy-dev] ERROR: PIP is not a legl parament of an
>> Ansible Play
>>
>>
>>
>> Hi Bill, can you describe what exactly you have done?
>>
>> What would be good is if you could post the beginning of your
>> tool_list.yml file,
>>
>> the command that you used to run the playbook, the version of galaxy and
>> the last commit
>>
>> of the playbook you are using (the last entry of `git log`).
>>
>> For any of this to work you should also be able manually install tools
>> from the toolshed.
>>
>> Does this work for you?
>>
>>
>>
>> On 21 April 2016 at 18:14, William Ge <w...@centrilliontech.com> wrote:
>>
>> Does anyone know why Ansible installation of the tools did not update the
>> shed_tools_conf.xml file to reflect the installed tools? How can I make the
>> tools installed with the Ansible playbook visible on the web front end?
>>
>> Thanks,
>>
>> Bill
>>
>>
>>
>> *From:* Enis Afgan [mailto:enis.af...@irb.hr]
>> *Sent:* Friday, April 8, 2016 9:19 AM
>>
>>
>> *To:* William Ge <w...@centrilliontech.com>
>> *Cc:* Marius van den Beek <m.vandenb...@gmail.com>;
>> galaxy-dev@lists.galaxyproject.org
>> *Subject:* Re: [galaxy-dev] ERROR: PIP is not a legl parament of an
>> Ansible Play
>>
>>
>>
>> The location of that dir is defined in shed_tool_conf.xml[.sample] and
>> defaults to ../shed_tools. The reasoning is described here, under item #2:
>> https://wiki.galaxyproject.org/DevNewsBriefs/2012_10_23#Tool_Shed
>>
>>
>>
>> On Thu, Apr 7, 2016 at 11:09 AM, William Ge <w...@centrilliontech.com>
>> wrote:
>>
>> Thanks, Enis!
>>
>> Yes, that line was uncommented with the option pointing to
>> “tool_conf.xml,shed_tool_conf.xml”. However, I noticed that the
>> “shed_tool_conf.xml” has not been changed after running the
>> ansible-playbook to install tools. One other thing: the shed_tools
>> directory was one level above the Galaxy subdirectories: i.e., all
>> subdirectories (config, database, tool-data, tools, static, etc) are in
>> /home/galaxy/galaxy, while “shed_tools” is in /home/galaxy. Do not know why.
>>
>>
>>
>> Thanks,
>>
>> Bill
>>
>>
>>
>> *From:* Enis Afgan [mailto:enis.af...@irb.hr]
>> *Sent:* Thursday, April 7, 2016 7:06 AM
>> *To:* William Ge <w...@centrilliontech.com>
>> *Cc:* Marius van den Beek <m.vandenb...@gmail.com>;
>> galaxy-dev@lists.galaxyproject.org
>>
>>
>> *Subject:* Re: [galaxy-dev] ERROR: PIP is not a legl parament of an
>> Ansible Play
>>
>>
>>
>> Hi Bill,
>>
>> Do you have the value set in Galaxy's *$GALAXY_ROOT/config/galaxy.ini*
>> file for setting *tool_config_file *option? I believe this variable
>> should be set to a file other than the default **.sample*.
>>
>>
>>
>> On Wed, Apr 6, 2016 at 9:21 PM, William Ge <w...@centrilliontech.com>
>> wrote:
>>
>> Hi, Marius,
>>
>>
>>
>> I got ansible running and installed the tools on my local instance of
>> Galaxy. However, the tools are not shown on the tool panel on the web page.
>> Wonder if the tools has been installed in the wrong place, or something
>> else is wrong. Have been searching the Wiki and list without any resulst.
>> Please point me to the right directions.
>>
>>
>>
>> Thanks,
>>
>> Bill
>>
>>
>>
>> *From:* Marius van den Beek [mailto:m.vandenb...@gmail.com]
>> *Sent:* Friday, March 4, 2016 12:27 PM
>> *To:* William Ge <w...@centrilliontech.com>
>> *Cc:* Dannon Baker <dannon.ba...@gmail.com>;
>> galaxy-dev@lists.galaxyproject.org
>> *Subject:* Re: [galaxy-dev] ERROR: PIP is not a legl parament of an
>> Ansible Play
>>
>>
>>
>> On 4 March 2016 at 20:47, William Ge <w...@centrilliontech.com> wrote:
>>
>> Thanks a lot, Marius!
>>
>> Sure, you're welcome!
>>
>>
>>
>> I am a newbie to this complex system and want a quick clone/install
>> locally. I have spent over two weeks on the process. There are many
>> configuration files and environment variables or dependencies to sort out.
>> I wish the sample configuration files would include most of the options so
>> that new installation just needs to comment out or delete unwanted ones.
>>
>>
>>
>> The galaxy team definitely aims for this, and usually you should (tm) be
>> able to clone galaxy and use run.sh to get going.
>>
>> If you can tell us the steps where you were struggling we can try to
>> update or clarify the documentation (A lot of it is on the wiki).
>>
>> Anyway, here is the error I got:
>>
>> [galaxy@Pegasus ansible-galaxy-tools]$ python
>> files/install_tool_shed_tools.py -h
>> Traceback (most recent call last):
>> File "files/install_tool_shed_tools.py", line 49, in <module>
>> logging.captureWarnings(True) # Capture HTTPS warngings from urllib3
>> AttributeError: 'module' object has no attribute 'captureWarnings'
>>
>>
>>
>> If I run this after activating the galaxy_env and install ensible,
>> bioblend, argparse and importlib, the same error came up. I guess this is
>> Python 2.6 issue. Any solutions known?
>>
>>
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>>
>>
>>
>
>